Gandhi and Matthew, thank you for your hard work. I was working on upgrading libraries and fixing dependencies too. I would love to help with Spring dependency. For that reason, I have created issue: "upgrade Spring dependency from 3.1.2 to 4.x" (CTAKES-472 [1]).
Another great idea is the REST service, for that reason I created CTAKES-473 [2]. It was also requested by Chei Pen in CTAKES-188 [3]. I would like to know if you settled already to any framework (e.g. Jersey vs CXF) and if you also manage the dictionaries and different profiles through the API. The last important idea I get is the Dockerfile, which sounds great for the community to just test and play with cTAKES without the need of building and exploring the source code. I was testing your work Matthew, and I think it is a great start. What is the community practice in code for features that require a longer time to be developed? Would it use a branch until it gets stable, or it is preferred to have it in trunk for a faster integration. The REST API feature, it will require a new module. Does the community prefers a name for it (i.e ctakes-rest-api) ? Alex [1] - https://issues.apache.org/jira/browse/CTAKES-472 [2] - https://issues.apache.org/jira/browse/CTAKES-473 [3] - https://issues.apache.org/jira/browse/CTAKES-188 On Sun, Oct 29, 2017 at 11:36 PM, Gandhi Rajan Natarajan < gandhi.natara...@arisglobal.com> wrote: > Matthew, > > Looking forward to hear from you. Please let me know if there are any > changes required to make the rest service more superior and performance > effective. Cheers. > > Regards, > Gandhi > > > -----Original Message----- > From: Matthew Vita [mailto:matthewvit...@gmail.com] > Sent: Sunday, October 29, 2017 9:30 PM > To: dev@ctakes.apache.org > Subject: Re: cTAKES as REST service [EXTERNAL] > > Sean, > > Ghandi and I have met and we both agreed that his solution is superior to > the one I was working on. Therefore, I will be helping to see this project > through to the end so we can get it into the codebase! > > Here are the remaining work items that I will be spending time on: > > 1. Get it running (I'm using Linux Mint) > 2. Test it out (including stress tests) > 3. Automate it to run in Docker (just need UMLS credentials) > 4. Make a call to > https://github.com/GoTeamEpsilon/cTAKES-Concept-Mention-Parser to get a > nice JSON payload that is easy to traverse (this can be an optional > switch, > of course - I believe it may be best to rewrite this in Java should > this be > included with the solution) > 5. Test the output in my web viewer: > https://github.com/GoTeamEpsilon/cTAKES-Friendly-Web-UI > 6. Work on preparing the solution for the cTAKES core codebase. I will > prepare it with a very rich README. > > I will provide my updates over the coming days. > > Thanks, > > Matthew Vita > www.matthewvita.com > > On Sun, Oct 29, 2017 at 7:47 AM, Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > Hi Gandhi, > > > > Thank you for the additional information. Having a reliable rest > > service included with ctakes would be a boon for everybody interested > > in web access. I look forward to checking out the info in github as > > soon as I am able. > > > > Thanks to you and Mathew both! > > > > Sean > > > > > > -----Original Message----- > > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > Sent: Sunday, October 29, 2017 5:44 AM > > To: dev@ctakes.apache.org > > Subject: RE: cTAKES as REST service [EXTERNAL] > > > > Hi Sean, > > > > I feel it's better to upgrade cTAKES Spring version to 4x so that > > exposing it as rest service becomes seamless. Please find the github > > link that contains the proposed changes for Spring upgrade in cTAKES, > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github. > > com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes- > > 2DSVN-2Dsrc&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=cedfmyhdY7P3qZdiVB- > > gp0T0WinfllT61pLMqbP_Jyw&s=eMYiHpgQwJ5Zjc7-gW6qyAJ3AS3-H622ZVSJEJcgd8s > > &e= > > > > I have not tested the changes in ytex modules as I'm not sure how to > > go about that. > > > > Matthew Vita will be reviewing the changes. He is also reviewing and > > testing my rest service changes. He will provide more info to us once > > we are done with our testing. So that we can discuss about > > productizing the same. > > > > Regards, > > Gandhi > > > > > > -----Original Message----- > > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > > Sent: Friday, October 27, 2017 12:53 AM > > To: dev@ctakes.apache.org > > Subject: RE: cTAKES as REST service [EXTERNAL] > > > > Hi Gandhi, > > > > That sounds really great! Thank you for sharing the process! > > > > Sean > > > > -----Original Message----- > > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > Sent: Thursday, October 26, 2017 3:02 PM > > To: dev@ctakes.apache.org > > Subject: RE: cTAKES as REST service [EXTERNAL] > > > > Hi Sean, > > > > I'm glad to inform that I was able to upgrade cTAKES to Spring 4 in my > > sandbox. As you have mentioned, it is used by uima fit for firing some > > queries. > > > > To brief it, I did the following changes: > > > > 1) Changing SimpleJdbcTemplate to JdbcTemplate in uima modules > > 2) Changing Spring version in cTAKES root pom.xml > > 3) Adding Spring versions in ctakes type system, ctakes assertion, > > ctakes ytex and ctakes ytex web modules. > > > > Now I'm able to expose cTAKES as a rest service which takes the > > clinical text as Input and outputs the result. > > > > Hope it helps someone. > > > > Regards, > > Gandhi > > > > -----Original Message----- > > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > Sent: Wednesday, October 25, 2017 7:33 PM > > To: dev@ctakes.apache.org > > Subject: RE: cTAKES as REST service [EXTERNAL] > > > > Hi Sean, > > > > Thanks for the instant response. Will try to upgrade to Spring 4 and > > keep you posted about the progress. > > > > Regards, > > Gandhi > > > > > > -----Original Message----- > > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > > Sent: Wednesday, October 25, 2017 7:28 PM > > To: dev@ctakes.apache.org > > Subject: RE: cTAKES as REST service [EXTERNAL] > > > > Hi Gandhi, > > > > You can always build ctakes in your sandbox with spring 4 and see if > > it works. This may require some "maven magic"(overrides) on your > > part. If it does seem to work please create a jira item to upgrade the > spring version. > > Then hopefully before the next release somebody will thoroughly test > > an update. > > > > Offhand I don't know if or why spring is needed for ctakes itself. At > > a quick search it looks like uimafit requires it. Does anybody out > > there know what spring capabilities are used, directly or indirectly, > > by ctakes modules? > > > > Thanks, > > Sean > > > > -----Original Message----- > > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > Sent: Wednesday, October 25, 2017 9:20 AM > > To: dev@ctakes.apache.org > > Subject: cTAKES as REST service [EXTERNAL] > > > > Hi All, > > > > We have extended the cTAKES web application available under > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github. > > com_healthnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIFAg&c > > = qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=e5GMRO_ > > 5OwQhQrkfpV5fwBp7uG07tZVd1u_xJRo9wDs&s=meOj7MzEliqIQEhU_ > > FeQwEnsUrWFSzgk5ihSEzoGRCI&e= and added our custom annotator. We have > > tested the same and it works fine with CVD. But we are facing problems > > while trying to expose this as rest service. > > > > cTAKES uses Spring 3.1.2 version internally which don't have out of > > the box support for rest controller. Can we go ahead and update the > > spring version to 4x in cTAKES? Will it have any impact in the cTAKES > behavior? > > Also is there a better way to expose cTAKES as rest service apart from > > spring? > > > > Please advise. > > > > Regards, > > Gandhi > > > > This email and any files transmitted with it are confidential and > > intended solely for the use of the individual or entity to whom they are > addressed. > > If you are not the named addressee you should not disseminate, > > distribute or copy this e-mail. Please notify the sender or system > > manager by email immediately if you have received this e-mail by > > mistake and delete this e-mail from your system. 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If you are not the > > intended recipient you are notified that disclosing, copying, > > distributing or taking any action in reliance on the contents of this > > information is strictly prohibited and against the law. > > This email and any files transmitted with it are confidential and > > intended solely for the use of the individual or entity to whom they are > addressed. > > If you are not the named addressee you should not disseminate, > > distribute or copy this e-mail. Please notify the sender or system > > manager by email immediately if you have received this e-mail by > > mistake and delete this e-mail from your system. If you are not the > > intended recipient you are notified that disclosing, copying, > > distributing or taking any action in reliance on the contents of this > > information is strictly prohibited and against the law. > > This email and any files transmitted with it are confidential and > > intended solely for the use of the individual or entity to whom they are > addressed. > > If you are not the named addressee you should not disseminate, > > distribute or copy this e-mail. Please notify the sender or system > > manager by email immediately if you have received this e-mail by > > mistake and delete this e-mail from your system. If you are not the > > intended recipient you are notified that disclosing, copying, > > distributing or taking any action in reliance on the contents of this > > information is strictly prohibited and against the law. > > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you are not the named addressee you should not disseminate, distribute > or copy this e-mail. Please notify the sender or system manager by email > immediately if you have received this e-mail by mistake and delete this > e-mail from your system. If you are not the intended recipient you are > notified that disclosing, copying, distributing or taking any action in > reliance on the contents of this information is strictly prohibited and > against the law. >
